Increase your dosage for the Duramycin. And are you changing it out daily? It's light sensitive and it loses its effects within 24 hours of being exposed to light.

And honestly, I would cull the really sick animals that are chronic or don't recover fast. That's a sign of weak lungs and you don't want to breed animals with weak lungs. Rats already have so many respiratory issues.

And in the future, quarantine all new animals for at least 2 weeks.
I personally QT all new rats for 60 days. I once made the mistake of introducing a rat to my colony without QT and EVERYONE got sick. Never again.

Good luck!